Causes and Seasonality of Upper Respiratory Infections in Adults in Lesotho (2021-2022) (CORIAL).

Background: Upper respiratory tract infections cause morbidity and a high burden on healthcare systems worldwide, especially in low- and lower middle-income countries. Recent studies throughout Africa indicate seasonal patterns that deviate from those previously described in settings with temperate climates. Currently, there are no data available on pathogens causing upper respiratory infections and their seasonal patterns in Lesotho, Southern Africa. Methods: This cross-sectional nested study enrolled a randomly selected sample of adults presenting at St. Charles Mission Hospital, Seboche, in northern Lesotho between 01 August 2021 and 31 July 2022 with symptoms of respiratory infection (cough, shortness of breath or sore throat). As part of the parent study procedures, all participants underwent on-site SARS-CoV-2 rapid diagnostic testing (RDT), with a subset also receiving on-site PCR testing. Aliquots of the nasopharyngeal swab samples used for RDT were stored at -80 °C for subsequent multiplex PCR testing for 18 viruses and 4 bacteria, including SARS-CoV-2 (BIOFIRE RP 2.1 plus). Results: Of the 511 samples tested, 161 (31.5%) were positive for one pathogen and five (1.0%) for two pathogens. The most common pathogens were SARS-CoV-2 (41.6%), human rhinovirus/enterovirus (36.7%), non-COVID human coronaviruses (6.6%), parainfluenza viruses (6%) and influenza A and B viruses (4.8%). Human rhinoviruses/enteroviruses and SARS-CoV-2 showed a counter-cyclical pattern. Seasonal patterns were observed for human rhinoviruses/enteroviruses, human coronaviruses, parainfluenza and influenza A and B viruses. Conclusion: In this study, viral upper respiratory infections in Lesotho showed a pathogen spectrum and seasonal patterns similar to those described in other temperate climate settings.